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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcaactaagtgcgcatttttatttcgatccgatttttatgccacctactaggacctgtgattcacgcttttacaatcatttgcagGTTCGATACCAGAGCCGGAAATTACTCGCAGAGCAGCGTCCACGGGTCAAGGGCCAGTTTGTTCGTCAAGATCATAGCATCCAAGGAAGCTAGGGTCCAG

Basic information

species Zea mays
transcript GRMZM2G179024_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G179024_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os09g36220.2 (Oryza sativa), 3'ss of exon 7
-------gtaagcaactaagtgcgcatttttatttcgatccgattt-ttatgccacc---tactaggacctgtgattcacgcttttacaatcatttgcagGTTCGATACCAGAGCCGGAAATTACTCGCAGAGCAGCGTCCACGGGTCAAGGGCCAGTTTGTTCGTCAAGATCATAGCATCCAAGGAAGCTAGGGTCCAG
         ||||||||||    ||  ||||||| | |||| |||| || |    |    || ||| | ||||| || ||  ||||||| |  | ||||||| |||||||||||| ||||  |||| || |||||||| || ||||| ||||| ||||||||||| ||||||||| |  ||||||| ||||||||     
gtaggtcacaagcaactaatcttgccattttattccaatccaatttgttgtattgctgaatagtagaaactgtggtttacatttttacattgctgtgcagGTGCGATACCAGAGCAGGAAGCTACTAGCCGAGCAGCGACCGCGGGTTAAGGGTCAGTTTGTTCGGCAAGATCATGGTGTCCAAGGGAGCTAGGGCTGTC

upper sequence: GRMZM2G179024_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA07G05530.1 (Glycine max), 3'ss of exon 8
--------------------------------------------gtaagcaactaa-gtgcgcatttttatttcgatccga--tttttatgccacctacta--ggacctgtgattcacgc---ttttacaatcatttgcagGTTCGATACCAGAGCCGGAAATTACTCGCAGAGCAGCGTCCACGGGTCAAGGGCCAGTTTGTTCGTCAAGATCATAGCATC--CAAGGAAGCTAGGGTCCAG
                                             |    || | |  |      ||  | || | |  ||   |  |||  ||  |   |    |  | | ||| ||      | ||   || | |  |||||||||| || |||||||||  ||| ||||||||||| || ||||| ||||| |||||||| |||||| || ||        |   || ||| | |     
gtattataaccagcactaagtaaaaggctactttaagattatttatggtgaatttatatctatgattgcagttggcttggaaactcctatagcatgtttcactaaagatattattaacaagcactctaatttcttgtatagGTTCGATATCAAAGCCGGAAAAGACTGGCAGAGCAGCGGCCTCGGGTGAAGGGGCAGTTTGTACGTCAACATGATCATCCTGTCGCTGAGGCTGGTGGTG--

upper sequence: GRMZM2G179024_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA16G02050.1 (Glycine max), 3'ss of exon 7
---------------------------------------------------gtaagcaactaagtgcgcatttttatttcgatccgatttt-tatgccacctactaggacctgtgattcacgcttttacaatcatttgcagGTTCGATACCAGAGCCGGAAATTACTCGCAGAGCAGCGTCCACGGGTCAAGGGCCAGTTTGTTCGTCAAGATCATAG--CATCCAAGGAAGCTAGGGTCCAG
                                                    |    | ||| |   ||| ||   ||   | |   | |   |||   |     ||  | | | |   |    | ||   || | |  |||||||||| || |||||||||  ||| ||||||||||| || ||||| ||||| |||||||| || ||| || ||    ||| |   || ||| | |     
gtatcataaacagcacttagtaaaaggctactttaagattatttatggtgaatttatatctatgattgcagttggcttggaaactcctatagcatgtttcactaaagatcttattaacaagtactctaatttcttgtatagGTTCGATATCAAAGCCGGAAAAGACTGGCAGAGCAGCGGCCTCGGGTGAAGGGGCAGTTTGTACGACAACATAATCATCCATTCGCTGAGGCTGGTGGTG--

upper sequence: GRMZM2G179024_T01 (Zea mays), 3'ss of exon 7
lower sequence: Vv15s0048g02540.t01 (Vitis vinifera), 3'ss of exon 8
----gtaagcaactaagtgcgcatttttatttcgatccgatttttatgccacc-tactaggacctgtgattcacgcttt-tacaatcattt-----gcagGTTCGATACCAGAGCCGGAAATTACTCGCAGAGCAGCGTCCACGGGTCAAGGGCCAGTTTGTTCGTCAAGATCA---TAGCATCCAAGGAAGCTAGGGTCCAG
    |   | |   |  | |   ||||  |       | |  ||||| | |   |||  | |  |||       | ||  | |||   ||       |||||||||||||| ||| |||||   || |||||||||||||| || || || || ||||||||||| ||||  ||   |  ||  | |       | ||     
gttagcttggattcatctccaagttttgctgatagcgccaaatttatacaaggatacatgaagttgttccaattgtttaatgcaagttttcttaacacagGTTCGATACCAAAGCAGGAAAAGGCTTGCAGAGCAGCGTCCCCGAGTGAAAGGACAGTTTGTTCGACAAGTGCAGACTGACACTCCAACCGCTGATGGGT---

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|60341444|gb|DN208417.1|DN208417
EST:     CACTGAACAAGTTCCGGCTAAAGAGGAAGGATAGGTGCTTTGAGAAGAAG                         GTTCGATACCAGAGCCGGAAATTACTCGCAGAGCAGCGTCCACGGGTCAAG
genomic: CACTGAACAAGTTCCGGCTAAAGAGGAAGGATAGGTGCTTTGAGAAGAAGgtaagcaact ... tcatttgcagGTTCGATACCAGAGCCGGAAATTACTCGCAGAGCAGCGTCCACGGGTCAAG
EST: gi|32832897|gb|CD972575.1|CD972575
EST:     CACTGAACAAGTTCCGGCTAAAGAGGAAGGATAGGTGCTTTGAGAAGAAG                         GTTCGATACCAGAGCCGGAAATTACTCGCAGAGCAGCGTCCACGGGTCAAG
genomic: CACTGAACAAGTTCCGGCTAAAGAGGAAGGATAGGTGCTTTGAGAAGAAGgtaagcaact ... tcatttgcagGTTCGATACCAGAGCCGGAAATTACTCGCAGAGCAGCGTCCACGGGTCAAG
EST: gi|110201884|gb|EC883781.1|EC883781
EST:     CACTGAACAAGTTCCGGCTAAAGAGGAAGGATAGGTGCTTTGAGAAGAAG                         GTTCGATACCAGAGCCGGAAATTACTCGCAGAGCAGCGTCCACGGGTCAAG
genomic: CACTGAACAAGTTCCGGCTAAAGAGGAAGGATAGGTGCTTTGAGAAGAAGgtaagcaact ... tcatttgcagGTTCGATACCAGAGCCGGAAATTACTCGCAGAGCAGCGTCCACGGGTCAAG
EST: gi|32833367|gb|CD973045.1|CD973045
EST:     CACTGANCAAGTTCCGGCTAAAGAGGAAGGATAGGTGCTTTGAGAAGAAG                         GTTCGATACCAGAGCCGGAAATTACTCGCAGAGCAGCGTCCACGGGTCAAG
genomic: CACTGAACAAGTTCCGGCTAAAGAGGAAGGATAGGTGCTTTGAGAAGAAGgtaagcaact ... tcatttgcagGTTCGATACCAGAGCCGGAAATTACTCGCAGAGCAGCGTCCACGGGTCAAG
EST: gi|32833631|gb|CD973309.1|CD973309
EST:     GGATAGGTGCTTTGAGAAGAAG                         GTTCGATACCAGAGCCGGAAATTACTCGCAGAGCAGCGTCCACGGGTCAAG
genomic: GGATAGGTGCTTTGAGAAGAAGgtaagcaact ... tcatttgcagGTTCGATACCAGAGCCGGAAATTACTCGCAGAGCAGCGTCCACGGGTCAAG
EST: gi|211237343|gb|FL447339.1|FL447339
EST:     GAAGGATAGGTGCTTTGAGAAGAAG                         GTTCGATACCAGAGCCGGAAATTACTCGCAGAGCAGCGTCCACGGGTCAAG
genomic: GAAGGATAGGTGCTTTGAGAAGAAGgtaagcaact ... tcatttgcagGTTCGATACCAGAGCCGGAAATTACTCGCAGAGCAGCGTCCACGGGTCAAG
EST: gi|33098315|gb|CF058275.1|CF058275
EST:     CACTGAACAAGTTCCGGCTAAAGAGGAAGGATAGGTGCTTTGAGAAGAAG                         GTTCGATACCAGAGCCGGAAATTACTCGCAGAGCAGCGTCCACGGGTCAAG
genomic: CACTGAACAAGTTCCGGCTAAAGAGGAAGGATAGGTGCTTTGAGAAGAAGgtaagcaact ... tcatttgcagGTTCGATACCAGAGCCGGAAATTACTCGCAGAGCAGCGTCCACGGGTCAAG
EST: gi|211135211|gb|FL444569.1|FL444569
EST:     CACTGAACAAGTTCCGGCTAAAGAGGAAGGATAGGTGCTTTGAGAAGAAG                         GTTCGATACCAGAGCCGGAAATTACTCGCAGAGCAGCGTCCACGGGTCAAG
genomic: CACTGAACAAGTTCCGGCTAAAGAGGAAGGATAGGTGCTTTGAGAAGAAGgtaagcaact ... tcatttgcagGTTCGATACCAGAGCCGGAAATTACTCGCAGAGCAGCGTCCACGGGTCAAG
EST: gi|32835212|gb|CD974890.1|CD974890
EST:     CACTGAACAAGTTCCGGCTAAAGAGGAAGGATAGGTGCTTTGAGAAGAAG                         GTTCGATACCAGAGCCGGAAATTACTCGCAGAGCAGCGTCCACGGGTCAAG
genomic: CACTGAACAAGTTCCGGCTAAAGAGGAAGGATAGGTGCTTTGAGAAGAAGgtaagcaact ... tcatttgcagGTTCGATACCAGAGCCGGAAATTACTCGCAGAGCAGCGTCCACGGGTCAAG
EST: gi|211304182|gb|FL452363.1|FL452363
EST:     CACTGAACAAGTTCCGGCTAAAGAGGAAGGATAGGTGCTTTGAGAAGAAG                         GTTCGATACCAGAGCCGGAAATTACTCGCAGAGCAGCGTCCACGGGTCAAG
genomic: CACTGAACAAGTTCCGGCTAAAGAGGAAGGATAGGTGCTTTGAGAAGAAGgtaagcaact ... tcatttgcagGTTCGATACCAGAGCCGGAAATTACTCGCAGAGCAGCGTCCACGGGTCAAG
EST: gi|211273943|gb|FL428381.1|FL428381
EST:     CACTGAACAAGTTCCGGCTAAAGAGGAAGGATAGGTGCTTTGAGAAGAAG                         GTTCGATACCAGAGCCGGAAATTACTCGCAGAGCAGCGTCCACGGGTCAAG
genomic: CACTGAACAAGTTCCGGCTAAAGAGGAAGGATAGGTGCTTTGAGAAGAAGgtaagcaact ... tcatttgcagGTTCGATACCAGAGCCGGAAATTACTCGCAGAGCAGCGTCCACGGGTCAAG
EST: gi|87155248|gb|DY400037.1|DY400037
EST:     CACTGAACAAGTTCCGGCTAAAGAGGAAGGATAGGTGCTTTGAGAAGAAG                         GTTCGATACCAGAGCCGGAAATTACTCGCAGAGCAGCGTCCACGGGTCAAG
genomic: CACTGAACAAGTTCCGGCTAAAGAGGAAGGATAGGTGCTTTGAGAAGAAGgtaagcaact ... tcatttgcagGTTCGATACCAGAGCCGGAAATTACTCGCAGAGCAGCGTCCACGGGTCAAG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 71

TGAAACCCCAAGCGCCGAAGGGTCACGGCATCTGAGCCAGCGTGAGGCTGCACTGAACAAGTTCCGGCTAAAGAGGAAGGATAGGTGCTTTGAGAAGAAGgtaagcaact ... tcatttgcagGTTCGATACCAGAGCCGGAAATTACTCGCAGAGCAGCGTCCACGGGTCAAGGGCCAGTTTGTTCGTCAAGATCATAGCATCCAAGGAAGCTAGGGTCCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 79

TGAAACCCCAAGCGCCGAAGGGTCACGGCATCTGAGCCAGCGTGAGGCTGCACTGAACAAGTTCCGGCTAAAGAGGAAGGATAGGTGCTTTGAGAAGAAGgtaagcaact ... tcatttgcagGTTCGATACCAGAGCCGGAAATTACTCGCAGAGCAGCGTCCACGGGTCAAGGGCCAGTTTGTTCGTCAAGATCATAGCATCCAAGGAAGCTAGGGTCCAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 30

TGAAACCCCAAGCGCCGAAGGGTCACGGCATCTGAGCCAGCGTGAGGCTGCACTGAACAAGTTCCGGCTAAAGAGGAAGGATAGGTGCTTTGAGAAGAAGgtaagcaact ... tcatttgcagGTTCGATACCAGAGCCGGAAATTACTCGCAGAGCAGCGTCCACGGGTCAAGGGCCAGTTTGTTCGTCAAGATCATAGCATCCAAGGAAGCTAGGGTCCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 83

TGAAACCCCAAGCGCCGAAGGGTCACGGCATCTGAGCCAGCGTGAGGCTGCACTGAACAAGTTCCGGCTAAAGAGGAAGGATAGGTGCTTTGAGAAGAAGgtaagcaact ... tcatttgcagGTTCGATACCAGAGCCGGAAATTACTCGCAGAGCAGCGTCCACGGGTCAAGGGCCAGTTTGTTCGTCAAGATCATAGCATCCAAGGAAGCTAGGGTCCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatttttatgccacctactaggacctgtgattcacgcttttacaatcatttgcagGTTCGATACCAGAGCCGGAAATTACTCGCAGAGCAGCGTCCACGGGTCAAGGGCCAGTTTGTTCGTCAAGATCATAGCATCCAAGGAAGCTAGGGTCCAG
                                     ttttacaatcattt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcaactaagtgcgcatttttatttcgatccgatttttatgccacctactaggacctgtgattcacgcttttacaatcatttgcagGTTCGATACCAGAGCCGGAAATTACTCGCAGAGCAGCGTCCACGGGTCAAGGGCCAGTTTGTTCGTCAAGATCATAGCATCCAAGGAAGCTAGGGTCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA